Vaginal microbiome of women with adenomyosis: A case-control study/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-8
Subjects
- Location of subjects
- Thailand
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Upper part of vagina Cranial vagina,Pelvic part of vagina,Upper third of vagina,Upper vagina,Vagina upper part,Upper part of vagina,upper part of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Adenomyosis uterine corpus adenomyosis,Adenomyosis,adenomyosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adenomyosis patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with adenomoysis diagnosed using at least three diagnostic ultrasound-based criteria: globular shape uterus, asymmetric myometrial wall, thickening of the endometrial myometrial junction, hyperechoic striae along the sub-endometrial region, and presence of sub-endometrial microcyst
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not mentioned
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-8
Source: Fig 4
Description: Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance in the vaginal sample between adenomyosis and normal uterus.
Abundance in Group 1: increased abundance in adenomyosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alloscardovia | ||
| Coriobacteriaceae | ||
| Enhydrobacter | ||
| Faecalibacterium | ||
| Megamonas | ||
| Moraxellaceae | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Selenomonadaceae | ||
| Subdoligranulum | ||
| uncultured bacterium |
Revision editor(s): Andre, Peace Sandy, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-8
Source: Fig 4
Description: Linear discriminant analysis effect size (LEfSe) analysis of microbial abundance in the vaginal sample between adenomyosis and normal uterus.
Abundance in Group 1: decreased abundance in adenomyosis patients
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Fastidiosipila | ||
| Megasphaera | ||
| Oscillospiraceae | ||
| uncultured bacterium |
Revision editor(s): Andre, Peace Sandy, Folakunmi
